A variety of gastrointestinal pathological conditions in humans can be attributed, in total or in part, to micro-organisms, to inflammatory processes, or to a combination of both. For example, Clostridium difficile can cause pseudomembranous colitis, and can account for approximately 25% of cases of antibiotic-associated diarrhea, with an overall frequency of over 500 cases per 100,000 patients—a frequency which has risen markedly over the past decade. Risk factors and/or individuals susceptible for C. difficile-Associated Disease (CDAD) include extended hospitalization, advanced age, exposure to any of a number of antibiotics, immuno-suppressed individuals, individuals having IBD, individuals having CDAD or having had CDAD, and/or individuals undergoing chemotherapy. CDAD can be treated by discontinuation of the initiating antibiotic and administration of either vancomycin or metronidazole, both of which are highly effective. However, while treatment with antibiotic medication such as metronidazole and/or vancomycin can be effective against CDAD, treatment with both these agents is associated with about 20% rate of relapse. Additionally, the use of vancomycin is restricted due to concerns about vancomycin-resistant enterococci.
As another example of gastrointestinal pathological conditions, Helicobacter pylori is associated with a majority of peptic ulcers, and is implicated in gastritis and in gastric malignancies. As further examples, Shigella dysenteriae, Shigella flexneri, enterophathogenic Escherichia coli, Staphylococcus aureus, Enterococcus faecalis, Enterococcus faecium, Salmonella enterica, Campylobacter jejunum, Clostridium perfringens, Bacillus cereus, Vibrio cholera, Vibrio parahaemolyticus, and Giardia lamblia are enteric micro-organisms which can cause diarrhea, dysentery, and severe intestinal disease.